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How to trim adapters from paired end FASTQ data

This recipe performs data quality control on FASTQ data downloaded from SRA.

1 result • updated 9 months ago by Istvan Albert

This recipe performs data quality control on FASTQ data downloaded from SRA.

The recipe trims Illumina sequencing adapters from the end of sequences then performs a sliding window approach for correcting trailing low-quality sequences.

Finally, quality control reports are generated with fastqc.

For more information see the

Applied Bioinformatics online course
Biostar Handbook for system setup and other information.

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# The SRR run number.
SRA=SRR519926

# Stop the script on errors.
set -uex

# How many sequences to unpack.
N=10000

# Create directory to store the reads in.
mkdir -p reads

# Download 1000 reads from SRA.
fastq-dump --split-files -X $N -O reads  $SRA

# Make a directory for the fastqc reports
mkdir -p reports

# Run the fastqc report on the sra reads.
fastqc reads/*.fastq -o reports

# Create the adapter sequence used for trimming.
echo ">illumina" > adapter.fa
echo "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" >> adapter.fa

# Run trimmomatic on the data.
trimmomatic PE reads/${SRA}_1.fastq reads/${SRA}_2.fastq -baseout reads/${SRA}.trimmed.fq  ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20

# Run trimmomatic on the trimmed data.
fastqc reads/*.fq -o reports

# Delete the fastqc zip files to reduce clutter.
rm -f reports/*.zip

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